Xiang Chen

Ziwen Li, Xiang 'Anthony' Chen, Youngseung Jeon

Drug discovery (DD) has tremendously contributed to maintaining and improving public health. Hypothesizing that inhibiting protein misfolding can slow disease progression, researchers focus on target identification (Target ID) to find protein structures for drug binding. While Large Language Models (LLMs) and Retrieval-Augmented Generation (RAG) frameworks have accelerated drug discovery, integrating models into cohesive workflows remains challenging. We conducted a user study with drug discovery researchers to identify the applicability of LLMs and RAGs in Target ID. We identified two main findings: 1) an LLM should provide multiple Protein-Protein Interactions (PPIs) based on an initial protein and protein candidates that have a therapeutic impact; 2) the model must provide the PPI and relevant explanations for better understanding. Based on these observations, we identified three limitations in previous approaches for Target ID: 1) semantic ambiguity, 2) lack of explainability, and 3) short retrieval units. To address these issues, we propose GraPPI, a large-scale knowledge graph (KG)-based retrieve-divide-solve agent pipeline RAG framework to support large-scale PPI signaling pathway exploration in understanding therapeutic impacts by decomposing the analysis of entire PPI pathways into sub-tasks focused on the analysis of PPI edges.

Zirui Xu, Fuxun Yu, Chenchen Liu et al.

Nowadays, machine learning based Automatic Speech Recognition (ASR) technique has widely spread in smartphones, home devices, and public facilities. As convenient as this technology can be, a considerable security issue also raises -- the users' speech content might be exposed to malicious ASR monitoring and cause severe privacy leakage. In this work, we propose HASP -- a high-performance security enhancement approach to solve this security issue on mobile devices. Leveraging ASR systems' vulnerability to the adversarial examples, HASP is designed to cast human imperceptible adversarial noises to real-time speech and effectively perturb malicious ASR monitoring by increasing the Word Error Rate (WER). To enhance the practical performance on mobile devices, HASP is also optimized for effective adaptation to the human speech characteristics, environmental noises, and mobile computation scenarios. The experiments show that HASP can achieve optimal real-time security enhancement: it can lead an average WER of 84.55% for perturbing the malicious ASR monitoring, and the data processing speed is 15x to 40x faster compared to the state-of-the-art methods. Moreover, HASP can effectively perturb various ASR systems, demonstrating a strong transferability.